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Peng Y, Jiang L, Wu J, Yang J, Guo Z, Miao M, Peng Z, Chang M, Miao B, Liu H, Liang Y, Yin H, He Q, Liu X. Red Mud Potentially Alleviates Ammonia Nitrogen Inhibition in Swine Manure Anaerobic Digestion by Enhancing Phage-Mediated Ammonia Assimilation. Microorganisms 2025; 13:690. [PMID: 40142582 PMCID: PMC11944383 DOI: 10.3390/microorganisms13030690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 03/13/2025] [Accepted: 03/17/2025] [Indexed: 03/28/2025] Open
Abstract
Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria-phages interactions in this process remains poorly understood. Thus, this study investigated the impact of red mud on nitrogen metabolism in AD and characterized the phage and prokaryotic communities through a metagenomic analysis. The results showed that red mud significantly increased methane production by 23.1% and promoted the conversion of ammonia nitrogen into organic nitrogen, resulting in a 4.8% increase in total nitrogen. Simultaneously, it enriched the key microbial genera Methanothrix, Proteinophilum, and Petrimonas by 0.5%, 0.8%, and 2.7%, respectively, suggesting an enhancement in syntrophic acetate oxidation with greater ammonia tolerance. A viral metagenomic analysis identified seven nitrogen-metabolism-related auxiliary metabolic genes (AMGs), with glnA (encoding glutamine synthetase) being the most abundant. Compared to the control treatments, the red mud treatments led to a higher abundance of temperate phages and an increased number of AMGs. Furthermore, two new hosts carrying glnA (Mycolicibacteria smegmatis and Kitasatopola aureofaciens) were predicted, indicating that red mud expanded the host range of phages and promoted the spread of AMGs. Overall, our findings highlight the importance of phages in alleviating ammonia nitrogen inhibition and provide a novel understanding of the role of red mud in the AD of swine manure.
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Affiliation(s)
- Yulong Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Luhua Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Junzhao Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Jiejie Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Ziwen Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Manjun Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Zhiyuan Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Meng Chang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA;
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (Y.P.); (J.W.); (J.Y.); (Z.G.); (M.M.); (Z.P.); (M.C.); (B.M.); (H.L.); (Y.L.); (H.Y.); (X.L.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
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Novak V, van Winden MCM, Harwood TV, Neurath R, Kosina SM, Louie KB, Sullivan MB, Roux S, Zengler K, Mutalik VK, Northen TR. Virocell Necromass Provides Limited Plant Nitrogen and Elicits Rhizosphere Metabolites That Affect Phage Dynamics. PLANT, CELL & ENVIRONMENT 2025. [PMID: 40108761 DOI: 10.1111/pce.15456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 01/20/2025] [Accepted: 02/21/2025] [Indexed: 03/22/2025]
Abstract
Bacteriophages impact soil bacteria through lysis, altering the availability of organic carbon and plant nutrients. However, the magnitude of nutrient uptake by plants from lysed bacteria remains unknown, partly because this process is challenging to investigate in the field. In this study, we extend ecosystem fabrication (EcoFAB 2.0) approaches to study plant-bacteria-phage interactions by comparing the impact of virocell (phage-lysed) and uninfected 15N-labelled bacterial necromass on plant nitrogen acquisition and rhizosphere exometabolites composition. We show that grass Brachypodium distachyon derives some nitrogen from amino acids in uninfected Pseudomonas putida necromass lysed by sonication but not from virocell necromass. Additionally, the bacterial necromass elicits the formation of rhizosphere exometabolites, some of which (guanosine), alongside tested aromatic acids (p-coumaric and benzoic acid), show bacterium-specific effects on bacteriophage-induced lysis when tested in vitro. The study highlights the dynamic feedback between virocell necromass and plants and suggests that root exudate metabolites can impact bacteriophage infection dynamics.
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Affiliation(s)
- Vlastimil Novak
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michelle C M van Winden
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thomas V Harwood
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rachel Neurath
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Katherine B Louie
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew B Sullivan
- Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, Ohio, USA
| | - Simon Roux
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Karsten Zengler
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Program in Materials Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Zeng Q, Hu HW, Ge AH, Xiong C, Zhai CC, Duan GL, Han LL, Huang SY, Zhang LM. Plant-microbiome interactions and their impacts on plant adaptation to climate change. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2025; 67:826-844. [PMID: 39981843 DOI: 10.1111/jipb.13863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 01/20/2025] [Indexed: 02/22/2025]
Abstract
Plants have co-evolved with a wide range of microbial communities over hundreds of millions of years, this has drastically influenced their adaptation to biotic and abiotic stress. The rapid development of multi-omics approaches has greatly improved our understanding of the diversity, composition, and functions of plant microbiomes, but how global climate change affects the assembly of plant microbiomes and their roles in regulating host plant adaptation to changing environmental conditions is not fully known. In this review, we summarize recent advancements in the community assembly of plant microbiomes, and their responses to climate change factors such as elevated CO2 levels, warming, and drought. We further delineate the research trends and hotspots in plant-microbiome interactions in the context of climate change, and summarize the key mechanisms by which plant microbiomes influence plant adaptation to the changing climate. We propose that future research is urgently needed to unravel the impact of key plant genes and signal molecules modulated by climate change on microbial communities, to elucidate the evolutionary response of plant-microbe interactions at the community level, and to engineer synthetic microbial communities to mitigate the effects of climate change on plant fitness.
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Affiliation(s)
- Qing Zeng
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - An-Hui Ge
- Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chao Xiong
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Chang-Chun Zhai
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Gui-Lan Duan
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Li-Li Han
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Si-Yun Huang
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Zhou Z, Liu S, Saleem M, Liu F, Hu R, Su H, Dong D, Luo Z, Wu Y, Zhang Y, He Z, Wang C. Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process. BIORESOURCE TECHNOLOGY 2025; 419:132081. [PMID: 39826761 DOI: 10.1016/j.biortech.2025.132081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 01/13/2025] [Accepted: 01/14/2025] [Indexed: 01/22/2025]
Abstract
The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.
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Affiliation(s)
- Zhengyuan Zhou
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Songfeng Liu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA
| | - Fei Liu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Ruiwen Hu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Hualong Su
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Da Dong
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, Zhejiang A & F University, Lin'an 311300, China
| | - Zhiwen Luo
- State Environmental Protection Key Laboratory of Water Environmental Simulation and Pollution Control, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, China
| | - Yongjie Wu
- State Environmental Protection Key Laboratory of Water Environmental Simulation and Pollution Control, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, China
| | - Yan Zhang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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Cheng Z, He Y, Wang N, Wu L, Xu J, Shi J. Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025; 368:125787. [PMID: 39909332 DOI: 10.1016/j.envpol.2025.125787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Revised: 01/27/2025] [Accepted: 02/01/2025] [Indexed: 02/07/2025]
Abstract
Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha-1 and 1950 kg ha-1) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.
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Affiliation(s)
- Zhongyi Cheng
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou, 310058, China; Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, Écully, 69134, France
| | - Yan He
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou, 310058, China
| | - Nanxi Wang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Laosheng Wu
- Department of Environmental Sciences, University of California, Riverside, CA, 92521, USA
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiachun Shi
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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Van Goethem MW, Bezuidt OKI, Pierneef R, Vikram S, Hopkins DW, Aspray T, Hall G, Woodborne S, Hogg ID, Northen TR, Kong W, Daffonchio D, Cowan DA, Van de Peer Y, Delgado-Baquerizo M, Makhalanyane TP. Novel adaptive immune systems in pristine Antarctic soils. Sci Rep 2025; 15:2368. [PMID: 39827180 PMCID: PMC11742911 DOI: 10.1038/s41598-024-83942-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 12/18/2024] [Indexed: 01/22/2025] Open
Abstract
Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.
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Affiliation(s)
- Marc W Van Goethem
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - Oliver K I Bezuidt
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, DSI/NRF SARChI in Marine Microbiomics, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
| | - Rian Pierneef
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, DSI/NRF SARChI in Marine Microbiomics, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
| | - Surendra Vikram
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - David W Hopkins
- Scotland's Rural College, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Thomas Aspray
- School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Grant Hall
- Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | | | - Ian D Hogg
- Canadian High Arctic Research Station, Polar Knowledge Canada; and School of Science, University of Waikato, Waitkato, New Zealand
| | - Trent R Northen
- Molecular EcoSystems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Yves Van de Peer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Seville, Spain
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Hatfield, Pretoria, 0028, South Africa.
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, 7600, South Africa.
- The School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, 7600, South Africa.
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Zhao X, Qiao Q, Qin X, Zhao P, Li X, Xie J, Zhai F, Li Y. Viral community and antibiotic resistance genes carried by virus in soil microbial fuel cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 955:177260. [PMID: 39481552 DOI: 10.1016/j.scitotenv.2024.177260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 10/14/2024] [Accepted: 10/25/2024] [Indexed: 11/02/2024]
Abstract
Soil microbial fuel cells (MFCs) can control the horizontal transfer of antibiotic resistance genes (ARGs) by reducing the abundance of mobile genetic elements. However, little is known about the effect of soil MFCs on the horizontal transfer pathway of ARGs transduced by viruses. In this study, the average abundance of ARGs in soil MFCs was 11 % lower than that in the open-circuit control. Lower virus abundance in soil MFCs suggested less detriment of microbial communities. The structure of the viral community was respectively shifted by the introduction of electrodes and the stimulation of biocurrent, especially for the top three viral genera Oslovirus, Tequatrovirus and Incheonvrus in soil. The ARGs aac(6)-I, cat chloramphenicol acetyltransferase, qnrA and vanY were found as the highest health risk (Rank I), and their total abundance showed the lowest in MFCs, with a decrease of 91-99 % compared to the controls. As the main carrier of ARGs, the abundance of Caudoviricetes showed a significant positive correlation with ARGs. Viral integrase was identified respectively coexisting with arnA and vanR (Rank III) in the same contig, which might aggravate their horizontal transfer. Proteobacteria was the main host of viruses carrying ARGs, which exhibited the lowest abundance in the soil MFC. The genus Pseudomonas was the host of viruses carrying ARGs, whose amount reduced by soil MFCs. This study provides an insight into the bioelectrochemical control of ARGs horizontal transfer.
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Affiliation(s)
- Xiaodong Zhao
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci 030619, China; Shanxi Key Laboratory of Earth Surface Processes and Resource Ecology Security in Fenhe River Basin, Taiyuan Normal University, Yuci 030619, China
| | - Qingqing Qiao
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci 030619, China; Shanxi Key Laboratory of Earth Surface Processes and Resource Ecology Security in Fenhe River Basin, Taiyuan Normal University, Yuci 030619, China
| | - Xiaorui Qin
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci 030619, China; Shanxi Key Laboratory of Earth Surface Processes and Resource Ecology Security in Fenhe River Basin, Taiyuan Normal University, Yuci 030619, China
| | - Pengyu Zhao
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci 030619, China; Shanxi Key Laboratory of Earth Surface Processes and Resource Ecology Security in Fenhe River Basin, Taiyuan Normal University, Yuci 030619, China
| | - Xiaojing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China.
| | - Jun Xie
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci 030619, China; Shanxi Key Laboratory of Earth Surface Processes and Resource Ecology Security in Fenhe River Basin, Taiyuan Normal University, Yuci 030619, China
| | - Feihong Zhai
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci 030619, China; Shanxi Key Laboratory of Earth Surface Processes and Resource Ecology Security in Fenhe River Basin, Taiyuan Normal University, Yuci 030619, China.
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
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8
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Tariq M, Liu Y, Rizwan A, Shoukat CA, Aftab Q, Lu J, Zhang Y. Impact of elevated CO 2 on soil microbiota: A meta-analytical review of carbon and nitrogen metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175354. [PMID: 39117202 DOI: 10.1016/j.scitotenv.2024.175354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 07/17/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
In the face of 21st-century challenges driven by population growth and resource depletion, understanding the intricacies of climate change is crucial for environmental sustainability. This review systematically explores the interaction between rising atmospheric CO2 concentrations and soil microbial populations, with possible feedback effects on climate change and terrestrial carbon (C) cycling through a meta-analytical approach. Furthermore, it investigates the enzymatic activities related to carbon acquisition, gene expression patterns governing carbon and nitrogen metabolism, and metagenomic and meta-transcriptomic dynamics in response to elevated CO2 levels. The study reveals that elevated CO2 levels substantially influence soil microbial communities, increasing microbial biomass C and respiration rate by 15 % and upregulating genes involved in carbon and nitrogen metabolism by 12 %. Despite a 14 % increase in C-acquiring enzyme activity, there is a 5 % decrease in N-acquiring enzyme activity, indicating complex microbial responses to CO2 changes. Additionally, fungal marker ratios increase by 14 % compared to bacterial markers, indicating potential ecosystem changes. However, the current inadequacy of data on metagenomic and meta-transcriptomic processes underscores the need for further research. Understanding soil microbial feedback mechanisms is crucial for elucidating the role of rising CO2 levels in carbon sequestration and climate regulation. Consequently, future research should prioritize a comprehensive elucidation of soil microbial carbon cycling, greenhouse gas emission dynamics, and their underlying drivers.
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Affiliation(s)
- Maryam Tariq
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuexian Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ali Rizwan
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38000, Punjab, Pakistan
| | - Chaudhary Ammar Shoukat
- Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qudsia Aftab
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinfeng Lu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanxun Zhang
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing 101408
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9
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Ahmed A, Liu Y, He P, He P, Wu Y, Munir S, He Y. Bacillus quorum quenching shapes the citrus mycobiome through interkingdom signaling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 956:177074. [PMID: 39454793 DOI: 10.1016/j.scitotenv.2024.177074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 09/23/2024] [Accepted: 10/17/2024] [Indexed: 10/28/2024]
Abstract
Microbiomes are sustained through infinite yet mutually interacting microbial communities, with bacteria and fungi serving as the major constituents. In recent times, microbial interventions have become popular for microbiome manipulation to achieve sustainable goals. Whether and how the introduced biocontrol agent drives fungal microbial assemblages (mycobiome) and the role of interkingdom signaling in shaping the microbiome structure and function remain poorly understood. Here, we implemented wild-type (WT) Bacillus subtilis L1-21 and its quorum quenching (QQ) mutants (L1-21Δytnp, and L1-21Δyxel) individually and as consortia to explore the enrichment patterns of key mycobiome members in Huanglongbing (HLB) infected citrus compartments including leaf endosphere, root endosphere, and rhizosphere soil. The application of WT and its QQ mutants produced differential mycobiome enrichment across citrus compartments. Our findings reveal that application of WT B. subtilis enriched beneficial fungi such as Trichoderma (15.82 %) in leaf endosphere. In contrast, pathogenic fungi Fusarium (47.5 %) and Gibberella (0.47 %) involved in citrus root decline were adundant in the L1-21Δytnp treated root endosphere while Nigrospora (11 %) was predominant in L1-21Δyxel treated leaf endosphere, affirming the role of bacterial quorum sensing (QS) molecules in shaping the fungal community composition. In general, based on the fungal functional prediction, fungal pathogens were highly abundant in mutant-treated plants, particularly in leaf endosphere (L1-21Δytnp: 25 %; L1-21Δyxel: 36.35 %) compared to WT (20.93%). Additionally, some fungal members exhibited strong compartment specificity and both mutants induced distinct mycobiome shifts in rhizosphere soil, leaf, and root endopshere. In conclusion, B. subtilis QQ modifies bacterial QS networks facilitating beneficial fungi to establish, while loss of QQ leads to enrichment of pathogenic fungal groups. Our study provides a direct link of perception and regulation of mycobiome through bacterial-based QS and QQ system, and its association with disease outcomes.
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Affiliation(s)
- Ayesha Ahmed
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yinglong Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yixin Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
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10
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Jin M, Yu M, Feng X, Li Y, Zhang M. Characterization and comparative genomic analysis of a marine Bacillus phage reveal a novel viral genus. Microbiol Spectr 2024; 12:e0003724. [PMID: 39162547 PMCID: PMC11448403 DOI: 10.1128/spectrum.00037-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/12/2024] [Indexed: 08/21/2024] Open
Abstract
Bacillus pumilus exhibits substantial economic significance, with its metabolism, adaptability, and ecological functions regulated by its bacteriophages. Here, we isolated and characterized a novel temperate phage vB_BpuM-ZY1 from B. pumilus derived from mangrove sediments by mitomycin C induction. Phage vB_BpuM-ZY1 is a typical myophage, which has an icosahedral head with a diameter of 43.34 ± 2.14 nm and a long contractible tail with a length of 238.58 ± 5.18 nm. Genomic analysis indicated that vB_BpuM-ZY1 encodes genes for lysogeny control, and its life cycle may be intricately regulated by multiple mechanisms. vB_BpuM-ZY1 was predicted to employ P2-like 5'-extended-cos packaging strategy. In addition, genome-wide phylogenetic tree and proteome tree analyses indicated that vB_BpuM-ZY1 belongs to the Peduoviridae family but forms a separate branch at a deeper taxonomic level. Particularly, the comparative genomic analysis showed that vB_BpuM-ZY1 has less than 70% intergenomic similarities with its most similar phages. Thus, we propose that vB_BpuM-ZY1 is a novel Bacillus phage belonging to a new genus under the Peduoviridae family. The protein-sharing network analysis identified 44 vB_BpuM-ZY1-related phages. Interestingly, these evolutionarily related myophages infect a broad range of hosts across different phyla, which may be explained by the high structural variations of the host recognition domain in their central spike proteins. Collectively, our study will contribute to our understanding of Bacillus phage diversity and Bacillus-phage interactions, as well as provide essential knowledge for the industrial application of B. pumilus. IMPORTANCE Although recent metagenomics research has obtained a wealth of phage genetic information, much of it is considered "dark matter" because of the lack of similarity with known sequences in the database. Therefore, the isolation and characterization of novel phages will help to interpret the vast unknown viral metagenome data and improve our understanding of phage diversity and phage-host interactions. Bacillus pumilus shows high economic relevance due to its wide applications in biotechnology, industry, biopharma, and environmental sectors. Since phages influence the abundance, metabolism, evolution, fitness, and ecological functions of bacteria through complex interactions, the significance of isolation and characterization of novel phages infecting B. pumilus is apparent. In this study, we isolated and characterized a B. pumilus phage belonging to a novel viral genus, which provides essential knowledge for phage biology as well as the industrial application of B. pumilus.
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Affiliation(s)
- Min Jin
- />State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Meishun Yu
- />State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xuejin Feng
- />State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yinfang Li
- />State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Menghui Zhang
- />State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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11
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Wu R, Zimmerman AE, Hofmockel KS. The direct and indirect drivers shaping RNA viral communities in grassland soils. mSystems 2024; 9:e0009924. [PMID: 38980057 PMCID: PMC11334463 DOI: 10.1128/msystems.00099-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/31/2024] [Indexed: 07/10/2024] Open
Abstract
Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were Mitoviridae with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes. IMPORTANCE Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.
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Affiliation(s)
- Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Amy E. Zimmerman
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kirsten S. Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
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12
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Sun CL, Pratama AA, Gazitúa MC, Cronin D, McGivern BB, Wainaina JM, Vik DR, Zayed AA, Bolduc B, Wrighton KC, Rich VI, Sullivan MB. Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient. Environ Microbiol 2024; 26:e16665. [PMID: 39101434 DOI: 10.1111/1462-2920.16665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 05/16/2024] [Indexed: 08/06/2024]
Abstract
Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth-related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hosts in silico and found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses of Candidatus Methanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon-degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long-term observations enhance our understanding of soil viruses in the context of climate-relevant processes and provide opportunities to explore their role in terrestrial carbon cycling.
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Affiliation(s)
- Christine L Sun
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | | | - Dylan Cronin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Bridget B McGivern
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - James M Wainaina
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
| | - Dean R Vik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Kelly C Wrighton
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
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13
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Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024; 100:fiae052. [PMID: 38678007 PMCID: PMC11065364 DOI: 10.1093/femsec/fiae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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14
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Ma B, Wang Y, Zhao K, Stirling E, Lv X, Yu Y, Hu L, Tang C, Wu C, Dong B, Xue R, Dahlgren RA, Tan X, Dai H, Zhu YG, Chu H, Xu J. Biogeographic patterns and drivers of soil viromes. Nat Ecol Evol 2024; 8:717-728. [PMID: 38383853 DOI: 10.1038/s41559-024-02347-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.
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Affiliation(s)
- Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Erinne Stirling
- Agriculture and Food, CSIRO, Adelaide, South Australia, Australia
- Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, China
| | - Yijun Yu
- Arable Soil Quality and Fertilizer Administration Bureau of Zhejiang Province, Hangzhou, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Chao Tang
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Chuyi Wu
- School of Earth Sciences, Zhejiang University, Hangzhou, China
| | - Baiyu Dong
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Ran Xue
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hengyi Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Yong-Guan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
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15
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Wu H, Cui H, Fu C, Li R, Qi F, Liu Z, Yang G, Xiao K, Qiao M. Unveiling the crucial role of soil microorganisms in carbon cycling: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168627. [PMID: 37977383 DOI: 10.1016/j.scitotenv.2023.168627] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.
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Affiliation(s)
- Haowei Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Huiling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chenxi Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ran Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Fengyuan Qi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhelun Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Keqing Xiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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Zhao J, Nair S, Zhang Z, Wang Z, Jiao N, Zhang Y. Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments. THE ISME JOURNAL 2024; 18:wrae083. [PMID: 38709876 PMCID: PMC11126160 DOI: 10.1093/ismejo/wrae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/23/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g. deep-sea and hadal zones), indicating that macroalgal virospheres, despite being closest to us, are among the least understood. These viruses potentially maintain microbiome equilibrium critical for kelp health via lytic-lysogenic infections and the expression of folate biosynthesis genes. In-situ kelp mesocosm cultivation and metagenomic mining revealed that kelp holobiont profoundly reshaped surrounding seawater and sediment virus-prokaryote pairings through changing surrounding environmental conditions and virus-host migrations. Some kelp epiphytic viruses could even infect sediment autochthonous bacteria after deposition. Moreover, the presence of ample viral auxiliary metabolic genes for kelp polysaccharide (e.g. laminarin) degradation underscores the underappreciated viral metabolic influence on macroalgal carbon cycling. This study provides key insights into understanding the previously overlooked ecological significance of viruses within macroalgal holobionts and the macroalgae-prokaryotes-virus tripartite relationship.
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Affiliation(s)
- Jiulong Zhao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Shailesh Nair
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Zenghu Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zengmeng Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
| | - Yongyu Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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17
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Xiong L, Li Y, Zeng K, Wei Y, Li H, Ji X. Revealing viral diversity in the Napahai plateau wetland based on metagenomics. Antonie Van Leeuwenhoek 2023; 117:3. [PMID: 38153618 DOI: 10.1007/s10482-023-01912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.
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Affiliation(s)
- Lingling Xiong
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yanmei Li
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Kun Zeng
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Xiuling Ji
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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18
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Muscatt G, Cook R, Millard A, Bending GD, Jameson E. Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile. mBio 2023; 14:e0224623. [PMID: 38032184 PMCID: PMC10746233 DOI: 10.1128/mbio.02246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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19
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Yadav P, Quattrone A, Yang Y, Owens J, Kiat R, Kuppusamy T, Russo SE, Weber KA. Zea mays genotype influences microbial and viral rhizobiome community structure. ISME COMMUNICATIONS 2023; 3:129. [PMID: 38057501 DOI: 10.1038/s43705-023-00335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023]
Abstract
Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two Zea mays genotypes, parviglumis and B73, in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as rhizobiome microbial and viral community using 16S rRNA gene amplicon sequencing and genome resolved metagenomics. Our results demonstrated that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n = 7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vOTU) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbors genes capable of contributing to carbon cycling in the rhizosphere.
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Affiliation(s)
- Pooja Yadav
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Amanda Quattrone
- Complex Biosystems, University of Nebraska-Lincoln, Lincoln, NE, USA
- Texas A&M University, College Station, TX, USA
| | - Yuguo Yang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jacob Owens
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- University of Nebraska-Medical Center, Omaha, NE, USA
| | - Rebecca Kiat
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Sabrina E Russo
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Karrie A Weber
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Department of Earth and Atmospheric Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Daugherty Water for Food Global Institute, University of Nebraska, Lincoln, NE, USA.
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20
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Tian W, Zou B, Xu S, Xu Y, Zhang R, Li L, Jing Y, Wang M, Zhuang Y, Liu J, Liang C. Differences in microbial communities and potato growth in two soil types under organic cultivation. 3 Biotech 2023; 13:404. [PMID: 37982083 PMCID: PMC10656376 DOI: 10.1007/s13205-023-03832-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 10/23/2023] [Indexed: 11/21/2023] Open
Abstract
Organic agriculture plays a positive role in promoting genetic diversity, including living organisms, plants, and cultivated crops in the soil. However, few comparative studies reported whether different soil types were suitable for organic cultivation. In this study, loam and clay-loam soils under continuous organic cultivation were analyzed. The results showed that there were no significant differences between two soil types in soil pH, bulk density, total porosity, moisture content and three soil phases. The capillary porosity and organic matter content of loam were significantly higher than those of clay-loam. Compared with clay-loam soil, the contents of total nitrogen, phosphorus, potassium, calcium, zinc and silicon in loam soil were also significantly higher. The microbial diversity was higher in loam and the dominant microbes differed between the two soils. Glycosyl transferases and carbohydrate esterases were enriched in loam, whereas glycoside hydrolases and carbohydrate-binding modules were enriched in clay loam. The potato yield in loam was significantly higher than that in clay loam. Among the tuber quality indicators, the protein content of potatoes in loam was higher than that in clay-loam, but the reducing sugar content was lower for loam than for clay-loam. In conclusion, compared with clay loam, loam was more suitable for organic cultivation of potatoes on account of the high contents of nitrogen, phosphorus, and potassium and the rich microbial community, thus promoting a high yield of tubers. This study provided a theoretical reference for the selection of soil type suitable for organic cultivation.
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Affiliation(s)
- Wei Tian
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Benge Zou
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Shujing Xu
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Yinghao Xu
- Shandong Luyuan Weipin Agricultural High-Tech Co., Ltd., Laiyang, 265211 China
| | - Ruifeng Zhang
- Shandong Luyuan Weipin Agricultural High-Tech Co., Ltd., Laiyang, 265211 China
| | - Li Li
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Yali Jing
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Mengzhen Wang
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Yingyu Zhuang
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Jianlong Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109 China
| | - Chenglin Liang
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
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21
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Coclet C, Sorensen PO, Karaoz U, Wang S, Brodie EL, Eloe-Fadrosh EA, Roux S. Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. MICROBIOME 2023; 11:237. [PMID: 37891627 PMCID: PMC10604447 DOI: 10.1186/s40168-023-01666-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/07/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics' seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. RESULTS We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a "seed-bank" viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: "Kill-The-Winner" which proposes that lytic phages are actively infecting abundant bacteria, and "Piggyback-The-Persistent" which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. CONCLUSION Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry. Video Abstract.
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Affiliation(s)
- Clement Coclet
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Patrick O Sorensen
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shi Wang
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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22
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Liu X, Wang Y, Han L, Xia Y, Xie J. A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice. FEMS Microbiol Ecol 2023; 99:fiad113. [PMID: 37742208 DOI: 10.1093/femsec/fiad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant-pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV's detrimental effects on rice production.
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Affiliation(s)
- Xuewei Liu
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Yirong Wang
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Lijuan Han
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Yuxian Xia
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Jiaqin Xie
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
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23
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Cai H, Zhou Y, Li X, Xu T, Ni Y, Wu S, Yu Y, Wang Y. Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake. Viruses 2023; 15:2038. [PMID: 37896815 PMCID: PMC10611076 DOI: 10.3390/v15102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.
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Affiliation(s)
- Haoyun Cai
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Tianqi Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai 201306, China
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Abstract
Soil viruses are highly abundant and have important roles in the regulation of host dynamics and soil ecology. Climate change is resulting in unprecedented changes to soil ecosystems and the life forms that reside there, including viruses. In this Review, we explore our current understanding of soil viral diversity and ecology, and we discuss how climate change (such as extended and extreme drought events or more flooding and altered precipitation patterns) is influencing soil viruses. Finally, we provide our perspective on future research needs to better understand how climate change will impact soil viral ecology.
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Affiliation(s)
- Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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25
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Liu R, Li Z, Han G, Cun S, Hou D, Yu Z, Xue K, Liu X. Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process. WATER RESEARCH 2023; 232:119709. [PMID: 36764107 DOI: 10.1016/j.watres.2023.119709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02-0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.
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Affiliation(s)
- Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China; Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou City, Shandong Province, China.
| | - Zong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Ganghua Han
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Shujuan Cun
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Deyin Hou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China.
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Qin J, Ji B, Ma Y, Liu X, Wang T, Liu G, Li B, Wang G, Gao P. Diversity and potential function of pig gut DNA viruses. Heliyon 2023; 9:e14020. [PMID: 36915549 PMCID: PMC10006684 DOI: 10.1016/j.heliyon.2023.e14020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Viruses are ubiquitous in the gut of animals and play an important role in the ecology of the gut microbiome. The potential effects of these substances on the growth and development of the body are not fully known. Little is known about the effects of breeding environment on pig gut virome. Here, there are 3584 viral operational taxonomic units (vOTUs) longer than 5 kb identified by virus-enriched metagenome sequencing from 25 pig fecal samples. Only a small minority of vOTUs (11.16%) can be classified at the family level, and ∼50% of the genes could be annotated, supporting the concept of pig gut as reservoirs of substantial undescribed viral genetic diversity. The composition of pig gut virome in the six regions may be related to geography. There are only 20 viral clusters (VCs) shared among pig gut virome in six regions of Shanxi Province. These viruses rarely carry antibiotic resistance genes (ARGs). At the same time, they possess abundant auxiliary metabolic genes (AMGs) potentially involved in carbon, sulfur metabolism and cofactor biosynthesis, etc. This study has revealed the unique characteristics and potential function of pig gut DNA virome and established a foundation for the recognition of the viral roles in gut environment.
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Affiliation(s)
- Junjun Qin
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Bingzhen Ji
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Yijia Ma
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Xin Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tian Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
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Viral and Bacterial Communities Collaborate through Complementary Assembly Processes in Soil to Survive Organochlorine Contamination. Appl Environ Microbiol 2023; 89:e0181022. [PMID: 36809072 PMCID: PMC10056961 DOI: 10.1128/aem.01810-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of viruses and hosts synergistically surviving under organochlorine pesticide (OCP) stress, we investigated the community assembly processes of viruses and bacteria at the taxon and functional gene levels in clean and OCP-contaminated soils in China using a combination of metagenomics/viromics and bioinformatics approaches. We observed a decreased richness of bacterial taxa and functional genes but an increased richness of viral taxa and auxiliary metabolic genes (AMGs) in OCP-contaminated soils (from 0 to 2,617.6 mg · kg-1). In OCP-contaminated soils, the assembly of bacterial taxa and genes was dominated by a deterministic process, of which the relative significance was 93.0% and 88.7%, respectively. In contrast, the assembly of viral taxa and AMGs was driven by a stochastic process, which contributed 83.1% and 69.2%, respectively. The virus-host prediction analysis, which indicated Siphoviridae was linked to 75.0% of bacterial phyla, and the higher migration rate of viral taxa and AMGs in OCP-contaminated soil suggested that viruses show promise for the dissemination of functional genes among bacterial communities. Taken together, the results of this study indicated that the stochastic assembly processes of viral taxa and AMGs facilitated bacterial resistance to OCP stress in soils. Moreover, our findings provide a novel avenue for understanding the synergistic interactions between viruses and bacteria from the perspective of microbial ecology, highlighting the significance of viruses in mediating bioremediation of contaminated soils. IMPORTANCE The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities. This is the first study that aimed to understand the assembly process of bacterial and viral communities under OCP stress. The findings of this study provide information about microbial community responses to OCP stress and reveal the collaborative interactions between viral and bacterial communities to resist pollutant stress. Thereby, we highlight the importance of viruses in soil bioremediation from the perspective of community assembly.
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Abstract
The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.
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29
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Puxty RJ, Millard AD. Functional ecology of bacteriophages in the environment. Curr Opin Microbiol 2023; 71:102245. [PMID: 36512900 DOI: 10.1016/j.mib.2022.102245] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Bacteriophages are as ubiquitous as their bacterial hosts and often more abundant. Understanding how bacteriophages control their bacterial host populations requires a number of different approaches. Bacteriophages can control bacterial populations through lysis, drive evolution of bacterial immunity systems through infection, provide a conduit for horizontal gene transfer and alter host metabolism by carriage of auxiliary metabolic genes. Understanding and quantifying how bacteriophages drive these processes, requires both technological developments to take measurements in situ, and laboratory-based studies to understand mechanisms. Technological advances have allowed quantification of the number of infected cells in situ, revealing far-lower levels than expected. Understanding how observations in laboratory conditions relate to what occurs in the environment, and experimental confirmation of the predicted function of phage genes from observations in environmental omics data, remains challenging.
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Affiliation(s)
- Richard J Puxty
- University of Warwick, School of Life Sciences, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom.
| | - Andrew D Millard
- University of Leicester, Dept of Genetics and Genome Biology, University Road, Leicester, United Kingdom.
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30
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Bi L, Han LL, Du S, Yu DT, He JZ, Zhang LM, Hu HW. Cross-biome soil viruses as an important reservoir of virulence genes. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130111. [PMID: 36209605 DOI: 10.1016/j.jhazmat.2022.130111] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Viruses can significantly influence the composition and functions of their host communities and enhance host pathogenicity via the transport of virus-encoded virulence genes. However, the contribution of viral communities to the dissemination of virulence genes across various biomes across a large scale is largely unknown. Here, we constructed 29,283 soil viral contigs (SVCs) from viral size fraction metagenomes and public databases. A total of 1310 virulence genes were identified from 1164 SVCs in a wide variety of soil biomes, including grassland, agricultural and forest soils. The virulence gene gmd was the most abundant one, followed by csrA, evpJ, and pblA. A great proportion of viruses encoding virulence genes were uncharacterized. Virus-host linkage analysis revealed that most viruses were linked to only one bacterial genus, whereas several SVCs were associated with more than one bacterial genus and even two bacterial phyla, suggesting the potential risk of spreading virulence genes across different bacterial communities via viruses. Altogether, we provided new evidence for the prevalence of virulence genes in soil viruses across biomes, which advanced our understanding of the potential role of soil viruses in driving the pathogenesis of their hosts in terrestrial ecosystems.
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Affiliation(s)
- Li Bi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Shuai Du
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan-Ting Yu
- School of Geographical Sciences, Fujian Normal University, Fujian 350007, China
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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31
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Bhatt K, Suyal DC, Kumar S, Singh K, Goswami P. New insights into engineered plant-microbe interactions for pesticide removal. CHEMOSPHERE 2022; 309:136635. [PMID: 36183882 DOI: 10.1016/j.chemosphere.2022.136635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.
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Affiliation(s)
- Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA.
| | - Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
| | - Saurabh Kumar
- ICAR-Research Complex for Eastern Region, Patna, 800014, Bihar, India
| | - Kuldeep Singh
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004, India
| | - Priya Goswami
- Department of Biotechnology, Mangalayatan University, Uttar Pradesh, India
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32
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Wang S, Yu S, Zhao X, Zhao X, Mason-Jones K, Zhu Z, Redmile-Gordon M, Li Y, Chen J, Kuzyakov Y, Ge T. Experimental evidence for the impact of phages on mineralization of soil-derived dissolved organic matter under different temperature regimes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157517. [PMID: 35872205 DOI: 10.1016/j.scitotenv.2022.157517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/08/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Microbial mineralization of dissolved organic matter (DOM) plays an important role in regulating C and nutrient cycling. Viruses are the most abundant biological agents on Earth, but their effect on the density and activity of soil microorganisms and, consequently, on mineralization of DOM under different temperatures remains poorly understood. To assess the impact of viruses on DOM mineralization, we added soil phage concentrate (active vs. inactive phage control) to four DOM extracts containing inoculated microbial communities and incubated them at 18 °C and 23 °C for 32 days. Infection with active phages generally decreased DOM mineralization at day one and showed accelerated DOM mineralization later (especially from day 5 to 15) compared to that with the inactivated phages. Overall, phage infection increased the microbially driven CO2 release. Notably, while higher temperature increased the total CO2 release, the cumulative CO2 release induced by phage infection (difference between active phages and inactivated control) was not affected. However, higher temperatures advanced the response time of the phages but shortening its active period. Our findings suggest that bacterial predation by phages can significantly affect soil DOM mineralization. Therefore, higher temperatures may accelerate host-phage interactions and thus, the duration of C recycling.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Senxiang Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xiaoyan Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xiaolei Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Kyle Mason-Jones
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Zhenke Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Marc Redmile-Gordon
- Department of Environmental Horticulture, Royal Horticultural Society, Wisley GU23 6QB, UK
| | - Yong Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, 37077 Göttingen, Germany
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
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33
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Roux S, Emerson JB. Diversity in the soil virosphere: to infinity and beyond? Trends Microbiol 2022; 30:1025-1035. [PMID: 35644779 DOI: 10.1016/j.tim.2022.05.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/13/2023]
Abstract
Viruses are key members of Earth's microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome and metatranscriptome analyses that offer unprecedented windows into the soil virosphere. Given the emerging picture of high soil viral activity, diversity, and dynamics over short spatiotemporal scales, we then outline key eco-evolutionary processes that we hypothesize are the major diversity drivers for soil viruses. We argue that a community effort is needed to establish a 'global soil virosphere atlas' that can be used to address the roles of viruses in soil microbiomes and terrestrial biogeochemical cycles across spatiotemporal scales.
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Affiliation(s)
- Simon Roux
- DOE (Department of Energy) Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA; Genome Center, University of California, Davis, Davis, CA, USA.
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34
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Muscatt G, Hilton S, Raguideau S, Teakle G, Lidbury IDEA, Wellington EMH, Quince C, Millard A, Bending GD, Jameson E. Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere. MICROBIOME 2022; 10:181. [PMID: 36280853 PMCID: PMC9590211 DOI: 10.1186/s40168-022-01371-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/18/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. RESULTS Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. CONCLUSIONS Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sebastien Raguideau
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Graham Teakle
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Christopher Quince
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK.
- School of Natural Sciences, Bangor University, Bangor, UK.
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35
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Liao H, Li H, Duan CS, Zhou XY, Luo QP, An XL, Zhu YG, Su JQ. Response of soil viral communities to land use changes. Nat Commun 2022; 13:6027. [PMID: 36224209 PMCID: PMC9556555 DOI: 10.1038/s41467-022-33771-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/30/2022] [Indexed: 02/07/2023] Open
Abstract
Soil viruses remain understudied when compared to virus found in aquatic ecosystems. Here, we investigate the ecological patterns of soil viral communities across various land use types encompassing forest, agricultural, and urban soil in Xiamen, China. We recovered 59,626 viral operational taxonomic units (vOTUs) via size-fractioned viromic approach with additional mitomycin C treatment to induce virus release from bacterial fraction. Our results show that viral communities are significantly different amongst the land use types considered. A microdiversity analysis indicates that selection act on soil vOTUs, resulting in disparities between land use associated viral communities. Soil pH is one of the major determinants of viral community structure, associated with changes of in-silico predicted host compositions of soil vOTUs. Habitat disturbance and variation of soil moisture potentially contribute to the dynamics of putative lysogenic vOTUs. These findings provide mechanistic understandings of the ecology and evolution of soil viral communities in changing environments.
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Affiliation(s)
- Hu Liao
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Hu Li
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China
| | - Chen-Song Duan
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xin-Yuan Zhou
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Qiu-Ping Luo
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xin-Li An
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China
| | - Yong-Guan Zhu
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.9227.e0000000119573309State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
| | - Jian-Qiang Su
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
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Chu Y, Zhao Z, Cai L, Zhang G. Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis. ENVIRONMENTAL RESEARCH 2022; 210:112901. [PMID: 35227678 DOI: 10.1016/j.envres.2022.112901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
As the most numerous biological entities on Earth, viruses affect the microbial dynamics, metabolism and biogeochemical cycles in the aquatic ecosystems. Viral diversity and functions in ocean have been relatively well studied, but our understanding of viruses in mariculture systems is limited. To fill this knowledge gap, we studied viral diversity and potential biogeochemical impacts of sediments from four different prawn-mariculture ecosystems (mono-culture of prawn and poly-culture of prawn with jellyfish, sea cucumber, and clam) using a metagenomic approach with prior virus-like particles (VLPs) separation. We found that the order Caudovirales was the predominant viral category and accounted for the most volume (78.39% of classified viruses). Sediment viruses were verified to have a high diversity by using the construct phylogenetic tree of terL gene, with three potential novel clades being identified. Meanwhile, compared with viruses inhabiting other ecosystems based on gene-sharing network, our results revealed that mariculture sediments harbored considerable unexplored viral diversity and that maricultural species were potentially important drivers of the viral community structure. Notably, viral auxiliary metabolic genes were identified and suggested that viruses influence carbon and sulfur cycling, as well as cofactors/vitamins and amino acid metabolism, which indirectly participate in biogeochemical cycling. Overall, our findings revealed the genomic diversity and ecological function of viral communities in prawn mariculture sediments, and suggested the role of viruses in microbial ecology and biogeochemistry.
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Affiliation(s)
- Yunmeng Chu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China
| | - Zelong Zhao
- Shanghai BIOZERON Biotechnology Co., Ltd., Shanghai, 201800, China
| | - Lixi Cai
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China; Faculty of Basic Medicine, Putian University, Putian, 351100, Fujian, China
| | - Guangya Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China.
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Abstract
Microviruses encompass an astonishing array of small, single-stranded DNA phages that, due to the surge in metagenomic surveys, are now known to be prevalent in most environments. Current taxonomy concedes the considerable diversity within this lineage to a single family (the Microviridae), which has rendered it difficult to adequately and accurately assess the amount of variation that actually exists within this group. We amassed and curated the largest collection of microviral genomes to date and, through a combination of protein-sharing networks and phylogenetic analysis, discovered at least three meaningful taxonomic levels between the current ranks of family and genus. When considering more than 13,000 microviral genomes from recognized lineages and as-yet-unclassified microviruses in metagenomic samples, microviral diversity is better understood by elevating microviruses to the level of an order that consists of three suborders and at least 19 putative families, each with their respective subfamilies. These revisions enable fine-scale assessment of microviral dynamics: for example, in the human gut, there are considerable differences in the abundances of microviral families both between urban and rural populations and in individuals over time. In addition, our analysis of genome contents and gene exchange shows that microviral families carry no recognizable accessory metabolic genes and rarely, if ever, engage in horizontal gene transfer across microviral families or with their bacterial hosts. These insights bring microviral taxonomy in line with current developments in the taxonomy of other phages and increase the understanding of microvirus biology.
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Cao MM, Liu SY, Bi L, Chen SJ, Wu HY, Ge Y, Han B, Zhang LM, He JZ, Han LL. Distribution Characteristics of Soil Viruses Under Different Precipitation Gradients on the Qinghai-Tibet Plateau. Front Microbiol 2022; 13:848305. [PMID: 35464951 PMCID: PMC9022101 DOI: 10.3389/fmicb.2022.848305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are extremely abundant in the soil environment and have potential roles in impacting on microbial population, evolution, and nutrient biogeochemical cycles. However, how environment and climate changes affect soil viruses is still poorly understood. Here, a metagenomic approach was used to investigate the distribution, diversity, and potential biogeochemical impacts of DNA viruses in 12 grassland soils under three precipitation gradients on the Qinghai-Tibet Plateau, which is one of the most sensitive areas to climate change. A total of 557 viral operational taxonomic units were obtained, spanning 152 viral families from the 30 metagenomes. Both virus-like particles (VLPs) and microbial abundance increased with average annual precipitation. A significant positive correlation of VLP counts was observed with soil water content, total carbon, total nitrogen, soil organic matter, and total phosphorus. Among these biological and abiotic factors, SWC mainly contributed to the variability in VLP abundance. The order Caudovirales (70.1% of the identified viral order) was the predominant viral type in soils from the Qinghai-Tibet Plateau, with the Siphoviridae family being the most abundant. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes represented by glycoside hydrolases were identified, indicating that soil viruses may play a potential role in the carbon cycle on the Qinghai-Tibet Plateau. There were more diverse hosts and abundant CAZyme genes in soil with moderate precipitation. Our study provides a strong evidence that changes in precipitation impact not only viral abundance and virus–host interactions in soil but also the viral functional potential, especially carbon cycling.
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Affiliation(s)
- Miao-Miao Cao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Si-Yi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,The Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an, China
| | - Li Bi
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Shu-Jun Chen
- Information Technology Center, Tsinghua University, Beijing, China
| | - Hua-Yong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bing Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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Wang Y, Liu Y, Wu Y, Wu N, Liu W, Wang X. Heterogeneity of soil bacterial and bacteriophage communities in three rice agroecosystems and potential impacts of bacteriophage on nutrient cycling. ENVIRONMENTAL MICROBIOME 2022; 17:17. [PMID: 35387674 PMCID: PMC8985318 DOI: 10.1186/s40793-022-00410-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND As genetic entities infecting and replicating only in bacteria, bacteriophages can regulate the community structure and functions of their host bacteria. The ecological roles of bacteriophages in aquatic and forest environments have been widely explored, but those in agroecosystems remains limited. Here, we used metagenomic sequencing to analyze the diversity and interactions of bacteriophages and their host bacteria in soils from three typical rice agroecosystems in China: double cropping in Guangzhou, southern China, rice-wheat rotation cropping in Nanjing, eastern China and early maturing single cropping in Jiamusi, northeastern China. Enterobacter phage-NJ was isolated and its functions on soil nitrogen cycling and effect on soil bacterial community structure were verified in pot inoculation experiments and 16S rRNA gene sequencing. RESULTS Soil bacterial and viral diversity and predicted functions varied among the three agroecosystems. Genes detected in communities from the three agroecosystems were associated with typical functions: soil bacteria in Jiamusi were significantly enriched in genes related to carbohydrate metabolism, in Nanjing with xenobiotics biodegradation and metabolism, and in Guangzhou with virulence factors and scarce in secondary metabolite biosynthesis, which might lead to a significant occurrence of rice bacterial diseases. The virus community structure varies significantly among the three ecosystems, only 13.39% of the total viral species were shared by the three rice agroecosystems, 59.56% of the viral species were specific to one agroecosystem. Notably, over-represented auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in the viruses, which might assist host bacteria in metabolizing carbon, and 67.43% of these genes were present in Jiamusi. In bacteriophage isolation and inoculation experiments, Enterobacter bacteriophage-NJ reduced the nitrogen fixation capacity of soil by lysing N-fixing host bacteria and changed the soil bacterial diversity and community structure. CONCLUSION Our results showed that diversity and function predicted of paddy soil bacteria and viruses varied in the three agroecosystems. Soil bacteriophages can affect nutrient cycling by boosting host metabolism through the carried auxiliary metabolic genes (AMGs) and lysing the host bacteria that are involved in biogeochemical cycles. These findings form a basis for better understanding bacterial and bacteriophage diversity in different rice agroecosystems, laying a solid foundation for further studies of soil microbial communities that support ecofriendly production of healthy rice.
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Affiliation(s)
- Yajiao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding, 071000, China
| | - Yu Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuxing Wu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding, 071000, China
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Bi L, Yu DT, Han LL, Du S, Yuan CY, He JZ, Hu HW. Unravelling the ecological complexity of soil viromes: Challenges and opportunities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152217. [PMID: 34890674 DOI: 10.1016/j.scitotenv.2021.152217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
Viruses are extremely abundant and ubiquitous in soil, and significantly contribute to various terrestrial ecosystem processes such as biogeochemical nutrient cycling, microbiome regulation and community assembly, and host evolutionary dynamics. Despite their numerous dominance and functional importance, understanding soil viral ecology is a formidable challenge, because of the technological challenges to characterize the abundance, diversity and community compositions of viruses, and their interactions with other organisms in the complex soil environment. Viruses may engage in a myriad of biological interactions within soil food webs across a broad range of spatiotemporal scales and are exposed to various biotic and abiotic disturbances. Current studies on the soil viromes, however, often describe the complexity of their tremendous diversity, but lack of exploring their potential ecological roles. In this article, we summarized the major methods to decipher the ecology of soil viruses, discussed biotic and abiotic factors and global change factors that shape the diversity and composition of soil viromes, and the ecological roles of soil viruses. We also proposed a new framework to understand the ecological complexity of viruses from micro to macro ecosystem scales and to predict and unravel their activities in terrestrial ecosystems.
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Affiliation(s)
- Li Bi
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dan-Ting Yu
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China.
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuai Du
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng-Yu Yuan
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Han LL, Yu DT, Bi L, Du S, Silveira C, Cobián Güemes AG, Zhang LM, He JZ, Rohwer F. Distribution of soil viruses across China and their potential role in phosphorous metabolism. ENVIRONMENTAL MICROBIOME 2022; 17:6. [PMID: 35130971 PMCID: PMC8822697 DOI: 10.1186/s40793-022-00401-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China. RESULTS Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils. CONCLUSIONS The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.
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Affiliation(s)
- Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
| | - Dan-Ting Yu
- Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, Fujian, China.
| | - Li Bi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cynthia Silveira
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Ana Georgina Cobián Güemes
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
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Chen ML, An XL, Liao H, Yang K, Su JQ, Zhu YG. Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:13881-13890. [PMID: 34596377 DOI: 10.1021/acs.est.1c03847] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance is a global health concern. Long-term organic fertilization can influence the antibiotic resistome of agricultural soils, posing potential risks to human health. However, little is known about the contribution of viruses to the dissemination of antibiotic resistance genes (ARGs) in this context. Here, we profiled the viral communities and virus-associated ARGs in a long-term (over 10 years) organic fertilized field by viral metagenomic analysis. A total of 61,520 viral populations (viral operational taxonomic units, vOTUs) were retrieved, of which 21,308 were assigned at the family level. The viral community structures were significantly correlated with the bacterial community structures (P < 0.001) and the dosage of applied sewage sludge (r2 = 0.782). A total of 16 unique ARGs were detected in soil viromes, and the number of virus-associated ARG subtypes was higher in sewage sludge treatments (except for 1 SS) than others. The network analysis showed that the application of the organic fertilizer increased the bacteria-virus interactions, suggesting that the chances of ARG exchange between viruses and their hosts may increase. Overall, our results provide a novel understanding about virus-associated ARGs and factors affecting the profile of viral community in fertilized soil.
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Affiliation(s)
- Mo-Lian Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hu Liao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities. mSystems 2021; 6:e0120520. [PMID: 34402646 PMCID: PMC8407418 DOI: 10.1128/msystems.01205-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Candidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems but are rarely detected in soil. We concentrated particles of less than 0.2 μm in size from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in largely oxic environments such as soil. We recovered a diversity of CPR bacterial and some archaeal sequences but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms rarely reported in soil, as well as Saccharibacteria, Parcubacteria, and Microgenomates. CPR and archaea of the phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) were enriched 100- to 1,000-fold compared to that in bulk soil, in which we estimate each of these organisms comprises approximately 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also harbor ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We conclude that CPR bacteria and DPANN archaea are part of the rare soil biosphere and harbor unique metabolic platforms that potentially evolved to live symbiotically under relatively oxic conditions. IMPORTANCE Here, we investigated overlooked microbes in soil, Candidate Phyla Radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes. We found that some of these predicted symbionts, which have been largely studied in anaerobic systems, have acquired aerobic capacity via lateral transfer that may enable adaptation to oxic soil environments. We estimate that there are approximately 1 to 100 cells of each of these lineages per gram of soil, highlighting that the approach provides a window into the rare soil biosphere and its associated genetic potential.
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Kazantseva OA, Piligrimova EG, Shadrin AM. vB_BcM_Sam46 and vB_BcM_Sam112, members of a new bacteriophage genus with unusual small terminase structure. Sci Rep 2021; 11:12173. [PMID: 34108535 PMCID: PMC8190038 DOI: 10.1038/s41598-021-91289-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
One of the serious public health concerns is food contaminated with pathogens and their vital activity products such as toxins. Bacillus cereus group of bacteria includes well-known pathogenic species such as B. anthracis, B. cereus sensu stricto (ss), B. cytotoxicus and B. thuringiensis. In this report, we describe the Bacillus phages vB_BcM_Sam46 and vB_BcM_Sam112 infecting species of this group. Electron microscopic analyses indicated that phages Sam46 and Sam112 have the myovirus morphotype. The genomes of Sam46 and Sam112 comprise double-stranded DNA of 45,419 bp and 45,037 bp in length, respectively, and have the same GC-content. The genome identity of Sam46 and Sam112 is 96.0%, indicating that they belong to the same phage species. According to the phylogenetic analysis, these phages form a distinct clade and may be members of a new phage genus, for which we propose the name 'Samaravirus'. In addition, an interesting feature of the Sam46 and Sam112 phages is the unusual structure of their small terminase subunit containing N-terminal FtsK_gamma domain.
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Affiliation(s)
- Olesya A Kazantseva
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
| | - Emma G Piligrimova
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia
| | - Andrey M Shadrin
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
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Feng X, Yan W, Wang A, Ma R, Chen X, Lin TH, Chen YL, Wei S, Jin T, Jiao N, Zhang R. A Novel Broad Host Range Phage Infecting Alteromonas. Viruses 2021; 13:v13060987. [PMID: 34073246 PMCID: PMC8228385 DOI: 10.3390/v13060987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
Bacteriophages substantially contribute to bacterial mortality in the ocean and play critical roles in global biogeochemical processes. Alteromonas is a ubiquitous bacterial genus in global tropical and temperate waters, which can cross-protect marine cyanobacteria and thus has important ecological benefits. However, little is known about the biological and ecological features of Alteromonas phages (alterophages). Here, we describe a novel alterophage vB_AmeP-R8W (R8W), which belongs to the Autographiviridae family and infects the deep-clade Alteromonas mediterranea. R8W has an equidistant and icosahedral head (65 ± 1 nm in diameter) and a short tail (12 ± 2 nm in length). The genome size of R8W is 48,825 bp, with a G + C content of 40.55%. R8W possesses three putative auxiliary metabolic genes encoding proteins involved in nucleotide metabolism and DNA binding: thymidylate synthase, nucleoside triphosphate pyrophosphohydrolase, and PhoB. R8W has a rapid lytic cycle with a burst size of 88 plaque-forming units/cell. Notably, R8W has a wide host range, such that it can infect 35 Alteromonas strains; it exhibits a strong specificity for strains isolated from deep waters. R8W has two specific receptor binding proteins and a compatible holin-endolysin system, which contribute to its wide host range. The isolation of R8W will contribute to the understanding of alterophage evolution, as well as the phage-host interactions and ecological importance of alterophages.
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Affiliation(s)
- Xuejin Feng
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Wei Yan
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- College of Marine Science and Technology, China University of Geosciences, Wuhan 430074, China
| | - Anan Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Ta-Hui Lin
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Yi-Lung Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Tao Jin
- Guangzhou Magigene Biotechnology Co., Ltd., Guangzhou 510000, China;
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- Correspondence: (N.J.); (R.Z.)
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
- Correspondence: (N.J.); (R.Z.)
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Yee MO, Kim P, Li Y, Singh AK, Northen TR, Chakraborty R. Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions. Front Microbiol 2021; 12:625752. [PMID: 33841353 PMCID: PMC8032546 DOI: 10.3389/fmicb.2021.625752] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.
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Affiliation(s)
- Mon Oo Yee
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Kim
- CBRN Defense and Energy Technologies, Sandia National Laboratories, Livermore, CA, United States
| | - Yifan Li
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anup K. Singh
- CBRN Defense and Energy Technologies, Sandia National Laboratories, Livermore, CA, United States
| | - Trent R. Northen
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Zheng L, Liang X, Shi R, Li P, Zhao J, Li G, Wang S, Han S, Radosevich M, Zhang Y. Viral Abundance and Diversity of Production Fluids in Oil Reservoirs. Microorganisms 2020; 8:microorganisms8091429. [PMID: 32957569 PMCID: PMC7563284 DOI: 10.3390/microorganisms8091429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 11/16/2022] Open
Abstract
Viruses are widely distributed in various ecosystems and have important impacts on microbial evolution, community structure and function and nutrient cycling in the environment. Viral abundance, diversity and distribution are important for a better understanding of ecosystem functioning and have often been investigated in marine, soil, and other environments. Though microbes have proven useful in oil recovery under extreme conditions, little is known about virus community dynamics in such systems. In this study, injection water and production fluids were sampled in two blocks of the Daqing oilfield limited company where water flooding and microbial flooding were continuously used to improve oil recovery. Virus-like particles (VLPs) and bacteria in these samples were extracted and enumerated with epifluorescence microscopy, and viromes of these samples were also sequenced with Illumina Hiseq PE150. The results showed that a large number of viruses existed in the oil reservoir, and VLPs abundance of production wells was 3.9 ± 0.7 × 108 mL-1 and virus to bacteria ratio (VBR) was 6.6 ± 1.1 during water flooding. Compared with water flooding, the production wells of microbial flooding had relative lower VLPs abundance (3.3 ± 0.3 × 108 mL-1) but higher VBR (7.9 ± 2.2). Assembled viral contigs were mapped to an in-house virus reference data separate from the GenBank non-redundant nucleotide (NT) database, and the sequences annotated as virus accounted for 35.34 and 55.04% of total sequences in samples of water flooding and microbial flooding, respectively. In water flooding, 7 and 6 viral families were identified in the injection and production wells, respectively. In microbial flooding, 6 viral families were identified in the injection and production wells. The total number of identified viral species in the injection well was higher than that in the production wells for both water flooding and microbial flooding. The Shannon diversity index was higher in the production well of water flooding than in the production well of microbial flooding. These results show that viruses are very abundant and diverse in the oil reservoir's ecosystem, and future efforts are needed to reveal the potential function of viral communities in this extreme environment.
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Affiliation(s)
- Liangcan Zheng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.L.); (M.R.)
| | - Rongjiu Shi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Ping Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyi Zhao
- No. 2 Oil Production Company, Daqing Oilfield Limited Company, Daqing 163414, China; (J.Z.); (G.L.)
| | - Guoqiao Li
- No. 2 Oil Production Company, Daqing Oilfield Limited Company, Daqing 163414, China; (J.Z.); (G.L.)
| | - Shuang Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Siqin Han
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.L.); (M.R.)
| | - Ying Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- Correspondence:
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